uorf4u (version 0.4.0): a bioinformatics tool for annotation conserved upstream ORFs.

COMMAND-LINE PARAMETERS
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[POST-INSTALL DATA]
--data
    Creates the 'uorf4u_data' folder in the current working directory.
    The folder contains adjustable configuration files used by uorf4u
    (e.g. config, SD-aSD energies table, palettes...).
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[MANDATORY ARGUMENTS]
-an <accession_number>	
	Protein's RefSeq accession number.
  OR
-hl <accession_number1 [accession_number2, ...]>
	Space separated list of proteins accession numbers which will be used
	as list of homologous.
  OR
-hlf <file.txt>
	Path to a file with list of accession numbers. File format:
	one accession number per line, no header.
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[OPTIONAL ARGUMENTS]
-al <path_to/assemblies_list.tsv>
	Path to an assemblies list file (see documentation for details).
-ul <length>
    Length of upstream sequences to retrieve for homologous.
-bh <number_of_hits>
    Max number of blastp hits in homologous searching.
-at <aa|nt>
	Alignment type used by uorf4u for conserved ORFs searching [default: aa]
-asc
    Include alternative start codons in uORF annotation step.
    List of alternative start codons are taken from the ncbi genetic code.
-c <file.cfg>
	Path to a configuration file [default: internal].
-o <name> 
	Output dirname. It will be created if it's not exist.
	All output dirs will be then created in this folder
	[default: uorf4u_{current_date}; e.g. uorf4u_2022_07_25-20_41].
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[MISCELLANEOUS ARGUMENTS]
-h, --help
	Show this help message and exit
-v, --version
	Show program version
--debug
	Provide detailed stack trace for debugging purposes
--verbose 
	Show all progress messages

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[SIMPLE EXAMPLE WITH MINIMAL ARGUMENTS]
Searching for the known ErmC' uORF called ErmCL: 
uorf4u -an WP_001003263.1 -verbose